I'm pretty conflicted on this. The objectionableness of Dotcom doesn't factor into things but it seems pretty clear that Megaupload was built on piracy and that's not a good thing. IP owners do have rights. However, MU wasn't just piracy and there are a lot of IP owners using it who are getting screwed over - but these IP owners aren't in a position to use the US DOJ for their own bidding. I feel that Dotcom does have things to answer for; there is a case, not that he's necessarily guilty.
The way the DoJ are handling this, I hope the trial falls apart leaving them with maximum egg on their face. I hope the judge reminds them of their responsibilities, ethics and jurisdiction.